宏基因组分析7-binning(Maxbin,metaBAT,CONCOCT)

maxbin

https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html
安装

cd /home/llt/software
wget https://downloads.jbei.org/data/microbial_communities/MaxBin/getfile.php?MaxBin-2.2.6.tar.gz
mv 'getfile.php?MaxBin-2.2.6.tar.gz' MaxBin-2.2.6.tar.gz
tar -zxvf MaxBin-2.2.6.tar.gz
cd MaxBin-2.2.6/src
make
cd ..
apt-get install autoconf
./autobuild_auxiliary

使用

/home/llt/software/MaxBin-2.2.6/run_MaxBin.pl -contig /home/llt/experiment/data/clean/trim_strict/megahit_out/final.contigs.fa -out bins -reads /home/llt/experiment/data/clean/trim_strict/ssg1_1p_20m.fq -reads2 /home/llt/experiment/data/clean/trim_strict/ssg1_2p_20m.fq -thread 4 -plotmarker -markerset 40 -min_contig_length 300
/home/llt/software/MaxBin-2.2.6/run_MaxBin.pl -contig /home/llt/experiment/data/clean/subsamble_10m/trim/assembly/final.contigs.fa -out bins -abund /home/llt/experiment/data/clean/subsamble_10m/trim/bins.abund1 -abund2 /home/llt/experiment/data/clean/subsamble_10m/trim/bins.abund2 -thread 4 -plotmarker -markerset 40 -min_contig_length 300

metaBAT

https://bitbucket.org/berkeleylab/metabat
install

sudo apt install libboost-dev
sudo apt install scons
wget https://bitbucket.org/berkeleylab/metabat/downloads/metabat-static-binary-linux-x64_v2.12.1.tar.gz
tar xzvf metabat-static-binary-linux-x64_v2.12.1.tar.gz
cd metabat
/software/metabat/jgi_summarize_bam_contig_depths --outputDepth depth.txt /home/llt/experiment/data/clean/subsamble_30m/assembly_spades/ssg1_30m.sorted.bam
/software/metabat/metabat2 -i /home/llt/experiment/data/clean/subsamble_30m/assembly_spades/contigs.fasta -o bin -a /home/llt/experiment/data/clean/subsamble_30m/assembly_spades/metabat/depth.txt

CONCOCT

https://github.com/BinPro/CONCOCT
install

sudo aptinstall build-essential libgsl0-dev libgomp1
sudo apt install bedtools
sudo apt install picard-tools
sudo apt install bowtie2
sudo apt install parallel
pip install cython biopython pandas scikit-learn
wget https://github.com/BinPro/CONCOCT/archive/1.0.0.zip
unzip 1.0.0.zip
cd CONCOCT-1.0.0/
python setup.py install

usage

cut_up_fasta.py /home/llt/experiment/data/clean/subsamble_30m/assembly_spades/contigs.fasta -c 10000 -o 0 --merge_last -b contigs.bed > contigs.fa
concoct_coverage_table.py /home/llt/experiment/data/clean/subsamble_30m/assembly_spades/concoct/contigs.bed /home/llt/experiment/data/clean/subsamble_30m/assembly_spades/ssg1_30m.sorted.bam > coverage_table.tsv
concoct -t 8 --composition_file contigs.fa  --coverage_file coverage_table.tsv -b 1000/
merge_cutup_clustering.py 1000/clustering_gt1000.csv > 1000/clustering_merged.csv